We can announce finally we have tappAS published. To cite us you can do it using the following text:
tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing
Lorena de la Fuente, Ángeles Arzalluz-Luque, Manuel Tardáguila, Héctor del Risco, Cristina Martí, Sonia Tarazona, Pedro Salguero, Raymond Scott, Ana Alastrue-Agudo, Pablo Bonilla, Jeremy Newman, Lauren McIntyre, Victoria Moreno-Manzano, Ana Conesa
Genome Biology; doi: https://doi.org/10.1186/s13059-020-02028-w
Select tappAS file to download below. Latest tappAS version available is 1.0.3.
|tappAS v1.0.3||tappAS Application version 1.0.3||Filesize: 17.8Mb|
|Note: In tappAS 1.0.3 you have to delete your last tappAS (versions 0.99.15 or below) and its tappasWorkspace folder and create all the projects again. Thank you for your understanding.|
If you were working with your own annotation file, you can visit our
|Miscellaneous Files||install.pdf||tappAS Installation and Requirements||Filesize: 82.7K
||GFFs files||tappAS GFFs||If you would like to follow de [ISMB 2020 tutorial], you can find the example dataset here.||tappAS - ISMB 2020 tutorial data||Filesize: 6Mb
Note: You may download additional annotation files and demos from the application as needed.
|1.0.3||August 3, 2020|
-DFI Summary plots fixed. Now can detect the features come from Transcript or Protein annotation correctly.
-Minor DIU Analysis bug fixed when filter by proportion is used.
|1.0.2||July 23, 2020|
-GO annotation has been updated (July 17, 2020).
-Minor DFI Analysis bug fixed.
|1.0.1||May 12, 2020|
-GO annotation has been updated (May 2, 2020).
-DFI Analysis fixed for Time Course Experiments.
|1.0.0||March 6, 2020|
-Install packages automaticatly updated.
-Load projects it is now faster.
-Updated all Help Documentation.
-GO annotation has been updated (February 21, 2020).
-URLs updated to work with the new website.
-Minor bugs fixed.
-DEA for time-course analysis fixed.
-DFI Summary tables fixed.
-Violin plot in UTRL analysis fixed.
-FEA clustering fixed.
-GSEA clustering fixed.
-New Enriched Feature visualization in GSEA.
|0.99.15||September 25, 2019|
-Experiment type "Case-Control" now is called "Two-Group Comparison".
-Fixed DFI Result Summary drillDown option.
-New UTR Lengthening Analysis (UTRL).
-New R packages installation.
-Fixed R graphics in Windows computers.
-Fixed FDA graphics.
-Updated DPA Analysis (Now it works for genes with multiple isoforms and no NDM transcripts).
-Updated DPA HeatMap (Two-Group Comparison).
-Updated all JavaFX visualizations.
-Updated help dialogs.
-GO annotation has been updated (July 1, 2019).
Time Course Experiments
-Minor correction in FDA.
-Now, DEA analysis shows P-Value and R square as a columns.
-Now, you can export ranked list in DEA analysis.
-Fixed DFI Graphics.
-Fixed DPA Graphics.
-Now, GSEA allows you to select our own tappAS ranked lists.
-Fixed GSEA mdgsa.
-Minor bugs fixed.
|0.99.14||June 28, 2019|
| -Now if a transcript is NMD, it won't shown protein. |
-New R visualization packages added to tappAS.
-Fixed: tappAS couldn't load a custom project if you modified .gff file.
-Miscellaneous changes in all graphs (title size, axis...) and export quality.
-New FDA Combined ID Results (New combined FDA ID analysis when you run for the same Feature, the analysis with Genomic Position and Presence parameters.)
-New FDA Combined Results Summary.
-Now, DEA and DIU Combined results show switching in transcripts and proteins.
-Fixed DIU graph.
-Fixed DPA values in annotation files. You have to download again all the annotation and create the projects to work correctly.
-New DPA graph to compare DPAU between conditions.
-Fixed DFI for Time series.
-Fixed DFI gene visualization.
-Fixed FEA Summary Graph.
-Added new option to FEA Summary (at left-hand side menu).
-Now, FEA Analaysis can be run for multiple features.
-New, GSEA method (mdgsa).
-New, GSEA multivariant method (mdgsa) for GOTerms.
-New, GSEA multivariant Interactive Summary. (You can see how much a GOTerm is regulated by each ranked list.)
-Fixed GSEA search.
-Fixed, if you select don't normalize your data you can't run edgeR method in DEA. (Because need raw data and we can't verify your data is not already normalized).
-Now, when you export a graph, the gene name will be show in the name file.
-Fixed in all annotations miRNA feature by miRNA_Binding.
-Fixed add extra columns by ID or Description in each table.
-GO annotation has been updated (June 25, 2019).
|0.99.13||May 29, 2019|
| -Now, if there is a new version of tappAS you will be notified.|
-Some GFF features have been renamed.
-Creating a new project, not integer values are suported in CPM filter.
-Now, you can select if you want to normalize your expression matrix by TMM method.
-FDA can store different analysis results.
-Now, FDA support two kind of analyses. Collapsing by feature or by id.
-FDA graph has been improved.
-Fixed sorted of FDA columns.
-Fixed DEA. Now, if you chose NoiSeq method you can indicate your own Fold Change to consider differential expression.
-Now in DEA, you can show the number of isoforms column.
-DIU pie chart indicates percentage of major switching isoforms.
-Fixed DIU graph. Now the top 5 genes are labeled correctly.
-DFI can store different analysis results.
-Fixed DFI filter.
-DFI Gene Associations change to Co-DFI Associations.
-Fixed DPA Log2(FC) graph.
-Now, Genomic Position comparation works correctly in FDA and DFI.
-Now, in FDA and DFI analyses you have to choose to analyze by Genomic Position or Presence, and the features you can analyze change depending its nature.
-Structual_Information source has change to TranscriptAttributes.
-Fixed graph: Transcripts, Protein and Gene Per Chromo.
-GO annotation was update (May 9, 2019).
|0.99.12||February 18, 2019|
| -Now, you can download all the R packages you need automatically.|
-Now, you can copy transcript, protein, genomic and expression charts images to clipboard.
-New Demo with extra annotations.
-New FDA graph.
-New DPA expression columns.
-New DPA graph in DPA summary.
-Disable MDGA mehotd in GSEA.
-Replacing TotalChg column by Total Usage Change in DIU Analysis.
-Fixed DIU scatter plot.
-Fixed DPA Plot (Log2 Fold Change).
-Fixed GSEA parameter windows for low resolution screens.
-Minor correction in FEA (Combobox names).
-Minor correction in FDA (Graphs).
-Minor correction in DPA (Graphs).
-Minor correction in DFI (Graphs).
-GO annotation was update (February 17, 2019).
|0.99.11||January 07, 2019|
| -New using method in DFI analysis (old Genomic is totally update).|
-New summary graphics in DFI analysis for Case-Control experiment.
-Fixed DFI filtering.
-Fixed DPA analysis.
-Minor correction in DPA analysis (graphs and names).
-Modify TotalChange column by ΔDPAU (distal polyA usage) and ΔFI (feature inclusion).
-Minor correction in General Summary.
-GO annotation was update (December 28, 2018).
|0.99.10||November 23, 2018|
| -Minor DPA bugs fixed.|
-Now, Podium Change is named as Mayor Isoform/PolyA Switching.
-Now, DSA is named as Differential Isoform Usage (DIU).
-Now, FDSA is named as Differential Feature Inclusion (DFI).
-Added new filters in DIU, DFI and DPA (by fold change or proportion).
-Fixed color in NMD transcripts.
-The method edgeR was eliminated from DIU, DFI and DPA.
-GO annotation was update (October 25, 2018).
|0.99.09||October 11, 2018|
| -Now, NMD transcripts are a different color.|
-Changed colors visualization in transcripts and proteins.
-Fixed values of error marks.
-Fixed ordering in proteins and transcripts.
-Fixed multiple time series charts in DPA.
|0.99.08||September 18, 2018|
| -Error marks added to Expression Charts.|
-Now, you can run the Functional Diversity Analysis for a specific list of genes.
-Added DPA Gene Summary option.
-Minor correction in FEA.
-Minor correction in GSEA.
-Fixed image exportation for DPA and DEA clusters.
-Fixed column size in all analysis to show all the title.
-Fixed Protein name for CDS.
-Fixed visualization subtaps (Now, you can't see the same symbol for different sources).
|0.99.07||July 20, 2018|
| -New Differential PolyAdenilation Analysis (DPA) |
-New annotations files with structure information
-New background white color for all graphics
-New set of color for all graphics and new icon design
-Minor Podium Change bugs fixed
-Minor FDSA bugs fixed
-Minor FEA bugs fixed
-Minor DEA bugs in Case-Control fixed
|0.99.06||March 23, 2018|
| -Implemented new GSEA method to run analysis (MDGSA)|
-Implemented new automatic filtering and reduction for GOterms in GSEA and FEA
-Implemented Favored condition
-Fixed filter in DSA and FDSA
-Fixed FDSA features selection
-Fixed save chart in FDSA drill down
-Added information to run tappAS If your hardware are much lower than recommended
-Automatically save the directory for rankList in GSEA and FEA for next time
|0.99.05||February 20, 2018|
| -Implemented DSA for single and multiple series time-course|
-Implemented FDSA for single and multiple series time-course
-Implemented Podium Change for DSA and FDSA
-Fixed Expression Values Filter when you create a new project
|0.99.04||February 07, 2018|
| -Viewing gene online reference feature not available for user annotation files|
-Fixed "abort function" in almost all analysis
-Fixed expression charts icon
-Miscellaneous display theme changes
|0.99.03||February 05, 2018|
| -Automatically save the directory of all data for next time|
-Using new format for project parameters
-Miscellaneous internal changes
-Miscellaneous display theme changes
|0.99.02||January 26, 2018|
| -Fixed display of tab overflow names in tab pane menu|
-Fixed protein sort by expression level in gene data visualization
-Modified about dialog to show credits
-Miscellaneous display theme changes
|0.99.01||December 15, 2017|
| -Initial release of TAPPAS after name change from Transcript2GO - will use new tappasWorkpsace folder